Geckoe project page:

Gecko (Gene Expression: Computation and Knowledge Organization) is a complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community.

Access to Geckoe download and installation instructions:

Project files (tar/gzip/zip/etc)
Installation README file (also bundled in the main package in Project files).

Summary from BMC paper abstract (BMC Bioinformatics 2004, 5:195):

Based on a client-server architecture, with a centralized repository of typically many tens of thousands of Affymetrix scans, Gecko includes automatic processing pipelines for uploading data from remote sites, a data base, a computational engine implementing ~50 different analysis tools, and a client application. Among available analysis tools are clustering methods, principal component analysis, supervised classification including feature selection and cross-validation, multi-factorial ANOVA, statistical contrast calculations, and various post-processing tools for extracting data at given error rates or significance levels. On account of its open architecture, Gecko also allows for the integration of new algorithms. The Gecko framework is very general: non-Affymetrix and non-gene expression data can be analyzed as well. A unique feature of the Gecko architecture is the concept of the Analysis Tree (actually, a directed acyclic graph), in which all successive results in ongoing analyses are saved. This approach has proven invaluable in allowing a large (~100 users) and distributed community to share results, and to repeatedly return over a span of years to older and potentially very complex analyses of gene expression data.

Please note that this site is still under construction. As of today (~June 2005), upload of all the Gecko source code is complete, and full installation documentation is about 95% complete (in particular, we provide for full step-by-step installation instructions for a ``reference'' Linux platform). Please see the table below for a detailed status report of the in-progress uploading.

Source code has been uploaded into the CVS repository, and separately in the form of two standalone tar files -- for client and server installations (see links below for access to CVS repository and all project files). You will find the corresponding tar files under the packages:

geckoClient
geckoServer

We will periodically update the Upload Status table below. We will also create appropriate documentation for navigating within the repository. Thanks for your patience!

Access to Geckoe download and installation instructions (same links as above):

Project files (tar/gzip/zip/etc)
Installation README file (also bundled in the main package in Project files).

Main Gecko paper:

Gecko BMC paper (``GECKO: a complete large-scale gene expression analysis platform'', Joachim Theilhaber, Anatoly Ulyanov, Anish Malanthara, Jack Cole, Dapeng Xu, Robert Nahf, Michael Heuer, Christoph Brockel and Steven Bushnell, BMC Bioinformatics 2004, 5:195)

Additional SourceForge sites:

Some additional papers and reports describing methods implemented in Gecko:

Document	Comments
icc-model-theilhaber-9-24-2002-NEW.pdf	Preprint on the intraclass correlation (icc) model for ``renormalizing'' P-values obtained from analyses of variance (ANOVAs) on expression data. This approach adjusts for the artificial inflation of statistical significance due to correlations within the groups used in the ANOVA. We have found it essential in avoiding unchecked divergence of the number of genes selected, as sample sizes become large.
PFOLD-JCB-11-1-2001.pdf	JCB article on the PFOLD Bayesian ratio estimation algorithm.
GENNC-GR-theilhaber-1-15-2002.pdf	Gene expression nearest neighbor classifier, applied to classification of osteogenic genes.

Source code upload status: April 11, 2005:
Note: line numbers listed below include comments but exclude blank lines.
Current total source code uploaded is about 350,000 lines.

Code category	Location	Contents (app.)	Fraction loaded (app.)
Database/schema/SQL build	cvs/tar file	1 file ~2,000 lines	100%
Perl/CGI	cvs/tar file	96 files 130,000 lines	100%
Perl/excutables	cvs/tar file	172 files 55,600 lines	100%
Perl/library modules	cvs/tar file	67 files 77,300 lines	100%
C++/compute engines	cvs/tar file	52 C++ source files 9 major categories 45,700 lines	100%
Java/compute engines	cvs/tar file		100%
Java/servlets	cvs/tar file		100%
VB client	tar file		100%
Datalib (annotation and CDF files)	cvs/tar file		100%
Automated build and installation	cvs/tar file	master autoconf file master makefile	95%
Build and install documentation	cvs/tar file	master text doc (Linux reference install) example logs	95%